[Objective] Wheat leaf rust caused by Puccinia triticina (Pt) is one of the most serious wheat diseases worldwide. Urediniospores germination is the premise to ensure the normal infection of leaf rust. Therefore, we studied differential expression characteristics of germinating urediniospores, to provide a basis for revealing the mechanism of germination and its relationship with pathogenesis. [Methods] We used RNA-seq to analyze the differentially expressed genes at resting and germinated urediniospores of THTT pathotype. [Results] We found 4400 up-regulated unigenes and 5325 down-regulated unigenes at germination stage compared with resting urediniospores. GO enrichment analysis showed that the up-regulated differentially unigenes mainly referred to cellular process, the metabolic process of organic matter, signal transduction, single-organism process and catalytic enzyme activity etc. The down-regulated unigenes mainly referred to single-organism process, single-organism cellular process, the metabolic process of organic matter, catalytic activity etc. All differentially expressed unigenes referred to 109 pathways. We choose Mitogen-activated protein kinase (MAPK) signaling pathway and Soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNARE) interactions in vesicular transport, which are related with germinating. The results of quantitative analysis of 10 unigenes were consistent with the results of gene digital expression profiling. [Conclusion] The result discovered the significantly differential unigenes in germinated urediniospores and this lay a base for understanding the pathogenic mechanism of Pt.